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36 * \brief API for neighborhood searching for analysis.
38 * The main part of the API is the class gmx::AnalysisNeighborhood.
39 * See the class documentation for usage.
41 * The classes within this file can be used independently of the other parts
43 * The library also uses the classes internally.
45 * \author Teemu Murtola <teemu.murtola@gmail.com>
47 * \ingroup module_selection
49 #ifndef GMX_SELECTION_NBSEARCH_H
50 #define GMX_SELECTION_NBSEARCH_H
54 #include <boost/shared_ptr.hpp>
56 #include "gromacs/math/vec.h"
57 #include "gromacs/math/vectypes.h"
58 #include "gromacs/utility/arrayref.h"
59 #include "gromacs/utility/classhelpers.h"
60 #include "gromacs/utility/gmxassert.h"
61 #include "gromacs/utility/real.h"
71 class AnalysisNeighborhoodSearchImpl;
72 class AnalysisNeighborhoodPairSearchImpl;
75 class AnalysisNeighborhoodSearch;
76 class AnalysisNeighborhoodPairSearch;
79 * Input positions for neighborhood searching.
81 * This class supports uniformly specifying sets of positions for various
82 * methods in the analysis neighborhood searching classes
83 * (AnalysisNeighborhood and AnalysisNeighborhoodSearch).
85 * Note that copies are not made: only a reference to the positions passed to
86 * the constructors are kept. The caller is responsible to ensure that those
87 * positions remain in scope as long as the neighborhood search object requires
90 * Also note that in addition to constructors here, Selection and
91 * SelectionPosition provide conversions operators to this type. It is done
92 * this way to not introduce a cyclic dependency between the selection code and
93 * the neighborhood search code, which in turn allows splitting this search
94 * code into a separate lower-level module if desired at some point.
96 * Methods in this class do not throw.
99 * \ingroup module_selection
101 class AnalysisNeighborhoodPositions
105 * Initializes positions from a single position vector.
107 * For positions initialized this way, AnalysisNeighborhoodPair always
108 * returns zero in the corresponding index.
110 * This constructor is not explicit to allow directly passing an rvec
111 * to methods that accept positions.
113 AnalysisNeighborhoodPositions(const rvec &x)
114 : count_(1), index_(-1), x_(&x), exclusionIds_(NULL), indices_(NULL)
118 * Initializes positions from an array of position vectors.
120 AnalysisNeighborhoodPositions(const rvec x[], int count)
121 : count_(count), index_(-1), x_(x), exclusionIds_(NULL), indices_(NULL)
125 * Initializes positions from a vector of position vectors.
127 AnalysisNeighborhoodPositions(const std::vector<RVec> &x)
128 : count_(x.size()), index_(-1), x_(as_rvec_array(&x[0])),
129 exclusionIds_(NULL), indices_(NULL)
134 * Sets indices to use for mapping exclusions to these positions.
136 * The exclusion IDs can always be set, but they are ignored unless
137 * actual exclusions have been set with
138 * AnalysisNeighborhood::setTopologyExclusions().
140 AnalysisNeighborhoodPositions &
141 exclusionIds(ConstArrayRef<int> ids)
143 GMX_ASSERT(static_cast<int>(ids.size()) == count_,
144 "Exclusion id array should match the number of positions");
145 exclusionIds_ = ids.data();
149 * Sets indices that select a subset of all positions from the array.
151 * If called, selected positions from the array of positions passed to
152 * the constructor is used instead of the whole array.
153 * All returned indices from AnalysisNeighborhoodPair objects are
154 * indices to the \p indices array passed here.
156 AnalysisNeighborhoodPositions &
157 indexed(ConstArrayRef<int> indices)
159 count_ = indices.size();
160 indices_ = indices.data();
165 * Selects a single position to use from an array.
167 * If called, a single position from the array of positions passed to
168 * the constructor is used instead of the whole array.
169 * In contrast to the AnalysisNeighborhoodPositions(const rvec &)
170 * constructor, AnalysisNeighborhoodPair objects return \p index
173 * If used together with indexed(), \p index references the index array
174 * passed to indexed() instead of the position array.
176 AnalysisNeighborhoodPositions &selectSingleFromArray(int index)
178 GMX_ASSERT(index >= 0 && index < count_, "Invalid position index");
187 const int *exclusionIds_;
190 //! To access the positions for initialization.
191 friend class internal::AnalysisNeighborhoodSearchImpl;
192 //! To access the positions for initialization.
193 friend class internal::AnalysisNeighborhoodPairSearchImpl;
197 * Neighborhood searching for analysis tools.
199 * This class implements neighborhood searching routines for analysis tools.
200 * The emphasis is in flexibility and ease of use; one main driver is to have
201 * a common implementation of grid-based searching to avoid replicating this in
202 * multiple tools (and to make more tools take advantage of the significant
203 * performance improvement this allows).
205 * To use the search, create an object of this type, call setCutoff() to
206 * initialize it, and then repeatedly call initSearch() to start a search with
207 * different sets of reference positions. For each set of reference positions,
208 * use methods in the returned AnalysisNeighborhoodSearch to find the reference
209 * positions that are within the given cutoff from a provided position.
211 * initSearch() is thread-safe and can be called from multiple threads. Each
212 * call returns a different instance of the search object that can be used
213 * independently of the others. The returned AnalysisNeighborhoodSearch
214 * objects are also thread-safe, and can be used concurrently from multiple
215 * threads. It is also possible to create multiple concurrent searches within
219 * Generalize the exclusion machinery to make it easier to use for other cases
220 * than atom-atom exclusions from the topology.
223 * \ingroup module_selection
225 class AnalysisNeighborhood
228 //! Searching algorithm to use.
231 //! Select algorithm based on heuristic efficiency considerations.
232 eSearchMode_Automatic,
233 //! Use a simple loop over all pairs.
235 //! Use grid-based searching whenever possible.
239 //! Creates an uninitialized neighborhood search.
240 AnalysisNeighborhood();
241 ~AnalysisNeighborhood();
244 * Sets cutoff distance for the neighborhood searching.
246 * \param[in] cutoff Cutoff distance for the search
247 * (<=0 stands for no cutoff).
249 * Currently, can only be called before the first call to initSearch().
250 * If this method is not called, no cutoff is used in the searches.
254 void setCutoff(real cutoff);
256 * Sets the search to only happen in the XY plane.
258 * Z component of the coordinates is not used in the searching,
259 * and returned distances are computed in the XY plane.
260 * Only boxes with the third box vector parallel to the Z axis are
261 * currently implemented.
265 void setXYMode(bool bXY);
267 * Sets atom exclusions from a topology.
269 * The \p excls structure specifies the exclusions from test positions
270 * to reference positions, i.e., a block starting at `excls->index[i]`
271 * specifies the exclusions for test position `i`, and the indices in
272 * `excls->a` are indices of the reference positions. If `excls->nr`
273 * is smaller than a test position id, then such test positions do not
274 * have any exclusions.
275 * It is assumed that the indices within a block of indices in
276 * `excls->a` is ascending.
280 * \see AnalysisNeighborhoodPositions::exclusionIds()
282 void setTopologyExclusions(const t_blocka *excls);
284 * Sets the algorithm to use for searching.
286 * \param[in] mode Search mode to use.
288 * Note that if \p mode is \ref eSearchMode_Grid, it is still only a
289 * suggestion: grid-based searching may not be possible with the
290 * provided input, in which case a simple search is still used.
291 * This is mainly useful for testing purposes to force a mode.
295 void setMode(SearchMode mode);
296 //! Returns the currently active search mode.
297 SearchMode mode() const;
300 * Initializes neighborhood search for a set of positions.
302 * \param[in] pbc PBC information for the frame.
303 * \param[in] positions Set of reference positions to use.
304 * \returns Search object that can be used to find positions from
305 * \p x within the given cutoff.
306 * \throws std::bad_alloc if out of memory.
308 * Currently, the input positions cannot use
309 * AnalysisNeighborhoodPositions::selectSingleFromArray().
311 AnalysisNeighborhoodSearch
312 initSearch(const t_pbc *pbc,
313 const AnalysisNeighborhoodPositions &positions);
318 PrivateImplPointer<Impl> impl_;
322 * Value type to represent a pair of positions found in neighborhood searching.
324 * Methods in this class do not throw.
327 * \ingroup module_selection
329 class AnalysisNeighborhoodPair
332 //! Initializes an invalid pair.
333 AnalysisNeighborhoodPair() : refIndex_(-1), testIndex_(0), distance2_(0.0)
337 //! Initializes a pair object with the given data.
338 AnalysisNeighborhoodPair(int refIndex, int testIndex, real distance2,
340 : refIndex_(refIndex), testIndex_(testIndex), distance2_(distance2)
346 * Whether this pair is valid.
348 * If isValid() returns false, other methods should not be called.
350 bool isValid() const { return refIndex_ >= 0; }
353 * Returns the index of the reference position in the pair.
355 * This index is always the index into the position array provided to
356 * AnalysisNeighborhood::initSearch().
360 GMX_ASSERT(isValid(), "Accessing invalid object");
364 * Returns the index of the test position in the pair.
366 * The contents of this index depends on the context (method call) that
368 * If there was no array in the call, this index is zero.
370 int testIndex() const
372 GMX_ASSERT(isValid(), "Accessing invalid object");
376 * Returns the squared distance between the pair of positions.
378 real distance2() const
380 GMX_ASSERT(isValid(), "Accessing invalid object");
384 * Returns the shortest vector between the pair of positions.
386 * The vector is from the test position to the reference position.
388 const rvec &dx() const
390 GMX_ASSERT(isValid(), "Accessing invalid object");
402 * Initialized neighborhood search with a fixed set of reference positions.
404 * An instance of this class is obtained through
405 * AnalysisNeighborhood::initSearch(), and can be used to do multiple searches
406 * against the provided set of reference positions.
407 * It is possible to create concurrent pair searches (including from different
408 * threads), as well as call other methods in this class while a pair search is
411 * This class works like a pointer: copies of it point to the same search.
412 * In general, avoid creating copies, and only use the copy/assignment support
413 * for moving the variable around. With C++11, this class would best be
416 * Methods in this class do not throw unless otherwise indicated.
419 * Make it such that reset() is not necessary to call in code that repeatedly
420 * assigns the result of AnalysisNeighborhood::initSearch() to the same
421 * variable (see sm_distance.cpp).
424 * Consider merging nearestPoint() and minimumDistance() by adding the distance
425 * to AnalysisNeighborhoodPair.
428 * \ingroup module_selection
430 class AnalysisNeighborhoodSearch
434 * Internal short-hand type for a pointer to the implementation class.
436 * shared_ptr is used here to automatically keep a reference count to
437 * track whether an implementation class is still used outside the
438 * AnalysisNeighborhood object. Ownership currently always stays with
439 * AnalysisNeighborhood; it always keeps one instance of the pointer.
441 typedef boost::shared_ptr<internal::AnalysisNeighborhoodSearchImpl>
445 * Initializes an invalid search.
447 * Such an object cannot be used for searching. It needs to be
448 * assigned a value from AnalysisNeighborhood::initSearch() before it
449 * can be used. Provided to allow declaring a variable to hold the
450 * search before calling AnalysisNeighborhood::initSearch().
452 AnalysisNeighborhoodSearch();
454 * Internally initialize the search.
456 * Used to implement AnalysisNeighborhood::initSearch().
457 * Cannot be called from user code.
459 explicit AnalysisNeighborhoodSearch(const ImplPointer &impl);
462 * Clears this search.
464 * Equivalent to \c "*this = AnalysisNeighborhoodSearch();".
465 * Currently, this is necessary to avoid unnecessary memory allocation
466 * if the previous search variable is still in scope when you want to
467 * call AnalysisNeighborhood::initSearch() again.
472 * Returns the searching algorithm that this search is using.
474 * The return value is never AnalysisNeighborhood::eSearchMode_Automatic.
476 AnalysisNeighborhood::SearchMode mode() const;
479 * Check whether a point is within a neighborhood.
481 * \param[in] positions Set of test positions to use.
482 * \returns true if any of the test positions is within the cutoff of
483 * any reference position.
485 bool isWithin(const AnalysisNeighborhoodPositions &positions) const;
487 * Calculates the minimum distance from the reference points.
489 * \param[in] positions Set of test positions to use.
490 * \returns The distance to the nearest reference position, or the
491 * cutoff value if there are no reference positions within the
494 real minimumDistance(const AnalysisNeighborhoodPositions &positions) const;
496 * Finds the closest reference point.
498 * \param[in] positions Set of test positions to use.
499 * \returns The reference index identifies the reference position
500 * that is closest to the test positions.
501 * The test index identifies the test position that is closest to
502 * the provided test position. The returned pair is invalid if
503 * no reference position is within the cutoff.
505 AnalysisNeighborhoodPair
506 nearestPoint(const AnalysisNeighborhoodPositions &positions) const;
509 * Start a search to find reference positions within a cutoff.
511 * \param[in] positions Set of test positions to use.
512 * \returns Initialized search object to loop through all reference
513 * positions within the configured cutoff.
514 * \throws std::bad_alloc if out of memory.
516 AnalysisNeighborhoodPairSearch
517 startPairSearch(const AnalysisNeighborhoodPositions &positions) const;
520 typedef internal::AnalysisNeighborhoodSearchImpl Impl;
526 * Initialized neighborhood pair search with a fixed set of positions.
528 * This class is used to loop through pairs of neighbors within the cutoff
529 * provided to AnalysisNeighborhood. The following code demonstrates its use:
531 gmx::AnalysisNeighborhood nb;
532 nb.setCutoff(cutoff);
533 gmx::AnalysisNeighborhoodPositions refPos(xref, nref);
534 gmx::AnalysisNeighborhoodSearch search = nb.initSearch(pbc, refPos);
535 gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(selection);
536 gmx::AnalysisNeighborhoodPair pair;
537 while (pairSearch.findNextPair(&pair))
539 // <do something for each found pair the information in pair>
543 * It is not possible to use a single search object from multiple threads
546 * This class works like a pointer: copies of it point to the same search.
547 * In general, avoid creating copies, and only use the copy/assignment support
548 * for moving the variable around. With C++11, this class would best be
551 * Methods in this class do not throw.
554 * \ingroup module_selection
556 class AnalysisNeighborhoodPairSearch
560 * Internal short-hand type for a pointer to the implementation class.
562 * See AnalysisNeighborhoodSearch::ImplPointer for rationale of using
563 * shared_ptr and ownership semantics.
565 typedef boost::shared_ptr<internal::AnalysisNeighborhoodPairSearchImpl>
569 * Internally initialize the search.
571 * Used to implement AnalysisNeighborhoodSearch::startPairSearch().
572 * Cannot be called from user code.
574 explicit AnalysisNeighborhoodPairSearch(const ImplPointer &impl);
577 * Finds the next pair within the cutoff.
579 * \param[out] pair Information about the found pair.
580 * \returns false if there were no more pairs.
582 * If the method returns false, \p pair will be invalid.
584 * \see AnalysisNeighborhoodPair
585 * \see AnalysisNeighborhoodSearch::startPairSearch()
587 bool findNextPair(AnalysisNeighborhoodPair *pair);
589 * Skip remaining pairs for a test position in the search.
591 * When called after findNextPair(), makes subsequent calls to
592 * findNextPair() skip any pairs that have the same test position as
593 * that previously returned.
594 * This is useful if the caller wants to search whether any reference
595 * position within the cutoff satisfies some condition. This method
596 * can be used to skip remaining pairs after the first such position
597 * has been found if the remaining pairs would not have an effect on
600 void skipRemainingPairsForTestPosition();